9Q03

Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)

This is a non-PDB format compatible entry.

Summary for 9Q03

• Entry DOI: 10.2210/pdb9q03/pdb
• EMDB information: 72086
• Descriptor: B-cell lymphoma 6 protein, Protein cereblon, ZINC ION, ... (4 entities in total)
• Functional Keywords: cereblon, bcl6, ldd, degrader, e3, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 3
• Total formula weight: 87226.36

Authors

Zhu, J.,Fang, W.,Pagarigan, B. (deposition date: 2025-08-12, release date: 2025-10-15, Last modification date: 2025-11-05)

Primary citation

Shunatona, H.P.,Holmberg Douglas, N.,Rhodes, J.,Thomas, W.,Da Silva, D.,Gamez, J.,Groza, M.,Christoforou, A.,Zhu, J.,Johnson, S.,Dodd, D.,Huang, D.,Griffin, J.,Miseo, G.,Whitefield, B.,Weiss, D.,Rader, J.,Kuzu, E.,Leisten, J.,Del Rosario, J.,Shi, L.,Matyskiela, M.,Chamberlain, P.P.,Belmont, P.,Alexander, M.,Zapf, C.W.,Groocock, L.,Mortensen, D.S.
Discovery of Potent and Selective BCL6 Ligand-Directed Degrader (LDD), BCL6-760.
J.Med.Chem., 68:21502-21519, 2025

PubMed Abstract: The discovery of a potent and selective BCL6 ligand-directed degrader (LDD), BCL6-760 () is described. Through structure-activity relationships, the most potent heterobifunctional degraders of BCL6 were found to be those containing short aminopiperidine linkers in combination with an indazole-based cereblon (CRBN)-binding moiety (CBM). In vitro ADME profiling of potent molecules identified BCL6-760 as an ideal molecule for use in in vivo experiments due to its good passive permeability, solubility, and microsomal stability. Mechanistic studies confirmed that BCL6 degradation is CRBN mediated, and proteomic assessment indicates a clean and selective degradation profile. BCL6-760 exhibited good oral mouse PK and was capable of penetrant and sustained PD effects. At 60 mg/kg BID dosing, BCL6-760 achieves >90% BCL6 reduction and leads to an overall 64% tumor volume reduction in an OCI-LY-1 mouse xenograft efficacy model.

PubMed: 41055242
DOI: 10.1021/acs.jmedchem.5c01645

Experimental method

ELECTRON MICROSCOPY (3.15 Å)